1
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Wei Y, Chen AX, Lin Y, Wei T, Qiao B. Allosteric regulation in SARS-CoV-2 spike protein. Phys Chem Chem Phys 2024; 26:6582-6589. [PMID: 38329233 DOI: 10.1039/d4cp00106k] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/09/2024]
Abstract
Allosteric regulation is common in protein-protein interactions and is thus promising in drug design. Previous experimental and simulation work supported the presence of allosteric regulation in the SARS-CoV-2 spike protein. Here the route of allosteric regulation in SARS-CoV-2 spike protein is examined by all-atom explicit solvent molecular dynamics simulations, contrastive machine learning, and the Ohm approach. It was found that peptide binding to the polybasic cleavage sites, especially the one at the first subunit of the trimeric spike protein, activates the fluctuation of the spike protein's backbone, which eventually propagates to the receptor-binding domain on the third subunit that binds to ACE2. Remarkably, the allosteric regulation routes starting from the polybasic cleavage sites share a high fraction (39-67%) of the critical amino acids with the routes starting from the nitrogen-terminal domains, suggesting the presence of an allosteric regulation network in the spike protein. Our study paves the way for the rational design of allosteric antibody inhibitors.
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Affiliation(s)
- Yong Wei
- Department of Computer Science, High Point University, High Point, NC 27268, USA
| | - Amy X Chen
- Thomas Jefferson High School for Science and Technology, Alexandria, VA 22312, USA
| | - Yuewei Lin
- Computational Science Initiative, Brookhaven National Laboratory, Upton, NY 11973, USA
| | - Tao Wei
- Department of Chemical Engineering and Department of Biomedical Engineering, University of South Carolina, Columbia, SC 29208, USA.
| | - Baofu Qiao
- Department of Natural Sciences, Baruch College, City University of New York, New York, NY 10010, USA.
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2
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Kuehl NJ, Taylor MT. Rapid Biomolecular Trifluoromethylation Using Cationic Aromatic Sulfonate Esters as Visible-Light-Triggered Radical Photocages. J Am Chem Soc 2023; 145:22878-22884. [PMID: 37819426 PMCID: PMC11076010 DOI: 10.1021/jacs.3c08098] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/13/2023]
Abstract
Described here is a photodecaging approach to radical trifluoromethylation of biomolecules. This was accomplished by designing a quinolinium sulfonate ester that, upon absorption of visible light, achieves decaging via photolysis of the sulfonate ester to ultimately liberate free trifluoromethyl radicals that are trapped by π-nucleophiles in biomolecules. This photodecaging process enables protein and protein-interaction mapping experiments using trifluoromethyl radicals that require only 1 s reaction times and low photocage concentrations. In these experiments, aromatic side chains are labeled in an environmentally dependent fashion, with selectivity observed for tryptophan (Trp), followed by histidine (His) and tyrosine (Tyr). Scalable peptide trifluoromethylation through photodecaging is also demonstrated, where bespoke peptides harboring trifluoromethyl groups at tryptophan residues can be synthesized with 5-7 min reaction times and good yields.
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Affiliation(s)
- Nicholas J. Kuehl
- Department of Chemistry, University of Wyoming, Laramie, WY 82071, United States
| | - Michael T. Taylor
- Department of Chemistry & Biochemistry, University of Arizona, Tucson, AZ 85721, United States
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3
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Guo W, Lu T, Crisci R, Nagao S, Wei T, Chen Z. Determination of protein conformation and orientation at buried solid/liquid interfaces. Chem Sci 2023; 14:2999-3009. [PMID: 36937592 PMCID: PMC10016606 DOI: 10.1039/d2sc06958j] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2022] [Accepted: 02/09/2023] [Indexed: 02/16/2023] Open
Abstract
Protein structures at solid/liquid interfaces mediate interfacial protein functions, which are important for many applications. It is difficult to probe interfacial protein structures at buried solid/liquid interfaces in situ at the molecular level. Here, a systematic methodology to determine protein molecular structures (orientation and conformation) at buried solid/liquid interfaces in situ was successfully developed with a combined approach using a nonlinear optical spectroscopic technique - sum frequency generation (SFG) vibrational spectroscopy, isotope labeling, spectra calculation, and computer simulation. With this approach, molecular structures of protein GB1 and its mutant (with two amino acids mutated) were investigated at the polymer/solution interface. Markedly different orientations and similar (but not identical) conformations of the wild-type protein GB1 and its mutant at the interface were detected, due to the varied molecular interfacial interactions. This systematic strategy is general and can be widely used to elucidate protein structures at buried interfaces in situ.
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Affiliation(s)
- Wen Guo
- Department of Chemistry, University of Michigan 930 North University Avenue Ann Arbor 48109 Michigan USA
| | - Tieyi Lu
- Department of Chemistry, University of Michigan 930 North University Avenue Ann Arbor 48109 Michigan USA
| | - Ralph Crisci
- Department of Chemistry, University of Michigan 930 North University Avenue Ann Arbor 48109 Michigan USA
| | - Satoshi Nagao
- Graduate School of Science, University of Hyogo 3-2-1 Koto, Ako-gun Kamigouri-cho Hyogo 678-1297 Japan
| | - Tao Wei
- Department of Chemical Engineering, Howard University 2366 Sixth Street NW Washington 20059 DC USA
| | - Zhan Chen
- Department of Chemistry, University of Michigan 930 North University Avenue Ann Arbor 48109 Michigan USA
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4
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Hydration and antibiofouling of TMAO-derived zwitterionic polymers surfaces studied with atomistic molecular dynamics simulations. Colloids Surf A Physicochem Eng Asp 2022. [DOI: 10.1016/j.colsurfa.2022.129943] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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5
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Vijeesh V, Vysakh A, Jisha N, Latha M. Multispectroscopic binding studies and in silico docking analysis of interactions of malic acid with xanthine oxidase. J Mol Struct 2022. [DOI: 10.1016/j.molstruc.2022.133621] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/31/2022]
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6
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Chen J, Xu E, Wei Y, Chen M, Wei T, Zheng S. Graph Clustering Analyses of Discontinuous Molecular Dynamics Simulations: Study of Lysozyme Adsorption on a Graphene Surface. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2022; 38:10817-10825. [PMID: 36001808 DOI: 10.1021/acs.langmuir.2c01331] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Understanding the interfacial behaviors of biomolecules is crucial to applications in biomaterials and nanoparticle-based biosensing technologies. In this work, we utilized autoencoder-based graph clustering to analyze discontinuous molecular dynamics (DMD) simulations of lysozyme adsorption on a graphene surface. Our high-throughput DMD simulations integrated with a Go̅-like protein-surface interaction model makes it possible to explore protein adsorption at a large temporal scale with sufficient accuracy. The graph autoencoder extracts a low-dimensional feature vector from a contact map. The sequence of the extracted feature vectors is then clustered, and thus the evolution of the protein molecule structure in the absorption process is segmented into stages. Our study demonstrated that the residue-surface hydrophobic interactions and the π-π stacking interactions play key roles in the five-stage adsorption. Upon adsorption, the tertiary structure of lysozyme collapsed, and the secondary structure was also affected. The folding stages obtained by autoencoder-based graph clustering were consistent with detailed analyses of the protein structure. The combination of machine learning analysis and efficient DMD simulations developed in this work could be an important tool to study biomolecules' interfacial behaviors.
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Affiliation(s)
- Jing Chen
- College of Materials and Chemistry & Chemical Engineering, Chengdu University of Technology, Chengdu, Sichuan 610059, P. R. China
| | | | - Yong Wei
- Department of Computer Science, High Point University, High Point, North Carolina 27268, United States
| | | | - Tao Wei
- Department of Chemical Engineering, Howard University, Washington, D.C. 20059, United States
| | - Size Zheng
- College of Materials and Chemistry & Chemical Engineering, Chengdu University of Technology, Chengdu, Sichuan 610059, P. R. China
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7
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Sarker P, Sajib MSJ, Tao X, Wei T. Multiscale Simulation of Protein Corona Formation on Silver Nanoparticles: Study of Ovispirin-1 Peptide Adsorption. J Phys Chem B 2022; 126:601-608. [PMID: 35026946 DOI: 10.1021/acs.jpcb.1c08267] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The exposure of nanoparticles (NPs) to biofluids leads to the rapid coverage of proteins, named protein corona, which alters the NPs' chemicophysical and biological properties. Fundamental studies of the protein corona are thus critical to the increasing applications of NPs in nanotechnology and nanomedicines. The present work utilizes multiscale simulations of a model biological system, small ovispirin-1 peptides, and bare silver nanoparticles (AgNPs) to examine the NPs' size and surface hydrophilicity effects on formation dynamics and the structure of the peptide corona. Our simulations revealed the different adsorption dynamics of ovispirin-1 peptides on the NPs, including the direct adsorption of a single peptide and peptide aggregates and multistep adsorption, as well as an intermediate cycle of desorption and readsorption. Notably, the whole process of peptide adsorption on hydrophilic AgNP surfaces can be generalized as three stages: diffusion to the surface, initial landing via hydrophilic residues, and the final attachment. The decrease in AgNP's size leads to faster adsorption with more heterogeneous peptide interfacial dynamics, a denser and inhomogeneous peptide packing structure, and a wider distribution of adsorption orientations. Subsequent atomistic molecular dynamics simulations demonstrated that on the hydrophilic AgNP surfaces, adsorbed peptides display moderate changes in their secondary structure, resulting in further changes of corona composition, i.e., amino acid residue distribution on the surface.
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Affiliation(s)
- Pranab Sarker
- Department of Chemical Engineering, Howard University, Washington, D.C. 20059, United States
| | - Md Symon Jahan Sajib
- Department of Chemical Engineering, Howard University, Washington, D.C. 20059, United States
| | - Xiuping Tao
- Department of Chemistry, Winston-Salem State University, Winston-Salem, North Carolina 27110, United States
| | - Tao Wei
- Department of Chemical Engineering, Howard University, Washington, D.C. 20059, United States
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8
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Ying D, Tseng CY, Chen PW, Lo YH, Hall D. A 30.3 fA/√Hz Biosensing Current Front-End With 139 dB Cross-Scale Dynamic Range. IEEE TRANSACTIONS ON BIOMEDICAL CIRCUITS AND SYSTEMS 2021; 15:1368-1379. [PMID: 34727038 DOI: 10.1109/tbcas.2021.3124197] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
This paper presents an 8-channel array of low-noise (30.3 fA/√Hz) current sensing front-ends with on-chip microelectrode electrochemical sensors. The analog front-end (AFE) consists of a 1st-order continuous-time delta-sigma (CT ΔΣ) modulator that achieves 123 fA sensitivity over a 10 Hz bandwidth and 139 dB cross-scale dynamic range with a 2-bit programmable current reference. A digital predictor and tri-level pulse width modulated (PWM) current-steering DAC realize the equivalent performance of a multi-bit ΔΣ in an area- and power-efficient manner. The AFE consumes 50.3 µW and 0.11 mm2 per readout channel. The proposed platform was used to observe protein-ligand interactions in real-time using transient induced molecular electronic spectroscopy (TIMES), a label- and immobilization-free biosensing technique.
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9
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Zheng S, Sajib MSJ, Wei Y, Wei T. Discontinuous Molecular Dynamics Simulations of Biomolecule Interfacial Behavior: Study of Ovispirin-1 Adsorption on a Graphene Surface. J Chem Theory Comput 2021; 17:1874-1882. [PMID: 33586958 DOI: 10.1021/acs.jctc.0c01172] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Fundamental understanding of biomolecular interfacial behavior, such as protein adsorption at the microscopic scale, is critical to broad applications in biomaterials, nanomedicine, and nanoparticle-based biosensing techniques. The goal of achieving both computational efficiency and accuracy presents a major challenge for simulation studies at both atomistic and molecular scales. In this work, we developed a unique, accurate, high-throughput simulation method which, by integrating discontinuous molecular dynamics (DMD) simulations with the Go-like protein-surface interaction model, not only solves the dynamics efficiently, but also describes precisely the protein intramolecular and intermolecular interactions at the atomistic scale and the protein-surface interactions at the coarse-grained scale. Using our simulation method and in-house developed software, we performed a systematic study of α-helical ovispirin-1 peptide adsorption on a graphene surface, and our study focused on the effect of surface hydrophobic interactions and π-π stacking on protein adsorption. Our DMD simulations were consistent with full-atom molecular dynamics simulations and showed that a single ovispirin-1 peptide lay down on the flat graphene surface with randomized secondary structure due to strong protein-surface interactions. Peptide aggregates were formed with an internal hydrophobic core driven by strong interactions of hydrophobic residues in the bulk environment. However, upon adsorption, the hydrophobic graphene surface can break the hydrophobic core by denaturing individual peptide structures, leading to disassembling the aggregate structure and further randomizing the ovispirin-1 peptide's secondary structures.
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Affiliation(s)
- Size Zheng
- College of Materials and Chemistry & Chemical Engineering, Chengdu University of Technology, Chengdu, Sichuan 610059, P. R. China
| | - Md Symon Jahan Sajib
- Chemical Engineering Department, Howard University, Washington, D.C. 20059, United States
| | - Yong Wei
- Department of Computer Science and Information Systems, University of North Georgia, Dahlonega, Georgia 30597, United States
| | - Tao Wei
- Chemical Engineering Department, Howard University, Washington, D.C. 20059, United States
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10
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Wei Y, Chin K, Barge LM, Perl S, Hermis N, Wei T. Machine Learning Analysis of the Thermodynamic Responses of In Situ Dielectric Spectroscopy Data in Amino Acids and Inorganic Electrolytes. J Phys Chem B 2020; 124:11491-11500. [PMID: 33284009 DOI: 10.1021/acs.jpcb.0c09266] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Dielectric spectroscopy (DS) can be a robust in situ technique for geochemical applications. In this study, we applied deep-learning techniques to DS measurement data to enable rapid science interrogation and identification of electrolyte solutions containing salts and amino acids over a wide temperature range (20 to -60 °C). For the purpose of searching for signs of life, detecting amino acids is a fundamental high priority for field and planetary instruments as amino acids are one of the building blocks for life as we know it. A convolutional neural network (CNN) with channel-wise one-dimensional filters is proposed to fulfill the task, using the DS data of amino acid and inorganic salt solutions. Experimental results show that the CNN with two convolutional layers and one fully connected layer can effectively differentiate solutions containing amino acids from those containing salts in both the liquid and solid (water ice) states. To complement the experimental measurements and CNN analysis, the diffusive behaviors of ions (K+, Cl-, and OH-) were further discussed with atomistic molecular dynamics simulations performed in this work as well as the quantum simulation published in the literature. Combining DS with machine-learning techniques and simulations will greatly facilitate more real-time decision-making of mobility systems for future exploratory endeavors in other worlds beyond Earth.
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Affiliation(s)
- Yong Wei
- Department of Computer Science and Information Systems, University of North Georgia, Dahlonega, Georgia 30597, United States
| | - Keith Chin
- NASA Jet Propulsion Laboratory, California Institute of Technology, 4800 Oak Grove Drive, Pasadena, California 91109, United States
| | - Laura M Barge
- NASA Jet Propulsion Laboratory, California Institute of Technology, 4800 Oak Grove Drive, Pasadena, California 91109, United States
| | - Scott Perl
- NASA Jet Propulsion Laboratory, California Institute of Technology, 4800 Oak Grove Drive, Pasadena, California 91109, United States
| | - Ninos Hermis
- NASA Jet Propulsion Laboratory, California Institute of Technology, 4800 Oak Grove Drive, Pasadena, California 91109, United States
| | - Tao Wei
- Chemical Engineering Department, Howard University, Washington, D.C. 20059, United States
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11
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Jahan Sajib MS, Sarker P, Wei Y, Tao X, Wei T. Protein Corona on Gold Nanoparticles Studied with Coarse-Grained Simulations. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2020; 36:13356-13363. [PMID: 33124831 DOI: 10.1021/acs.langmuir.0c02767] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Understanding protein corona formation in an aqueous environment at the molecular and atomistic levels is critical to applications such as biomolecule-detection and drug delivery. In this work, we employed mesoscopic coarse-grained simulations to study ovispirin-1 and lysozyme protein coronas on bare gold nanoparticles. Our study showed that protein corona formation is governed by protein-surface and protein-protein interactions, as well as the surface hydrophobic effect. The corona structure was found to be dependent on protein types and the size of nanoparticles. Ovispirin proteins form homogeneous single-layered adsorption in comparison with the lysozyme's inhomogeneous multilayered aggregates on gold NP surfaces. The decrease in nanoparticle size leads to more angular degrees of freedom for protein adsorption orientation. Subsequent atomistic molecular dynamics simulations further demonstrate the loss of secondary structure of ovispirin upon adsorption and the heterogeneity of its local structure.
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Affiliation(s)
- Md Symon Jahan Sajib
- Department of Chemical Engineering, Howard University, Washington, D.C. 20059, United States
| | - Pranab Sarker
- Department of Chemistry, Winston-Salem State University, Winston-Salem, North Carolina 27110, United States
| | - Yong Wei
- Department of Computer Science and Information Systems, University of North Georgia, Dahlonega, Georgia 30597, United States
| | - Xiuping Tao
- Department of Chemistry, Winston-Salem State University, Winston-Salem, North Carolina 27110, United States
| | - Tao Wei
- Department of Chemical Engineering, Howard University, Washington, D.C. 20059, United States
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12
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Chou CH, Lim JC, Lai YH, Chen YT, Lo YH, Huang JJ. Characterizations of protein-ligand reaction kinetics by transistor-microfluidic integrated sensors. Anal Chim Acta 2020; 1110:1-10. [DOI: 10.1016/j.aca.2020.03.012] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2019] [Revised: 02/11/2020] [Accepted: 03/07/2020] [Indexed: 11/28/2022]
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13
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Chen PW, Tseng CY, Shi F, Bi B, Lo YH. Detecting Protein-Ligand Interaction from Integrated Transient Induced Molecular Electronic Signal (i-TIMES). Anal Chem 2020; 92:3852-3859. [PMID: 32045225 DOI: 10.1021/acs.analchem.9b05310] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Quantitative information about protein-ligand interactions is central to drug discovery. To obtain the quintessential reaction dissociation constant, ideally measurements of reactions should be performed without perturbations by molecular labeling or immobilization. The technique of transient induced molecular electrical signal (TIMES) has provided a promising technique to meet such requirements, and its performance in a microfluidic environment further offers the potential for high throughput and reduced consumption of reagents. In this work, we further the development by using integrated TIMES signal (i-TIMES) to greatly enhance the accuracy and reproducibility of the measurement. While the transient response may be of interest, the integrated signal directly measures the total amount of surface charge density resulted from molecules near the surface of electrode. The signals enable quantitative characterization of protein-ligand interactions. We have demonstrated the feasibility of i-TIMES technique using different biomolecules including lysozyme, N,N',N″-triacetylchitotriose (TriNAG), aptamer, p-aminobenzamidine (pABA), bovine pancreatic ribonuclease A (RNaseA), and uridine-3'-phosphate (3'UMP). The results show i-TIMES is a simple and accurate technique that can bring tremendous value to drug discovery and research of intermolecular interactions.
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Affiliation(s)
- Ping-Wei Chen
- Chemical Engineering Program, University of California San Diego, La Jolla, California 92093-0448, United States
| | - Chi-Yang Tseng
- Materials Science and Engineering Program, University of California San Diego, La Jolla, California 92093-0418, United States
| | - Fumin Shi
- InnoScounting LLC, Rockville, Maryland 20850-4432, United States
| | - Bo Bi
- InnoScounting LLC, Rockville, Maryland 20850-4432, United States
| | - Yu-Hwa Lo
- Chemical Engineering Program, University of California San Diego, La Jolla, California 92093-0448, United States.,Materials Science and Engineering Program, University of California San Diego, La Jolla, California 92093-0418, United States.,Electrical and Computer Engineering Department, University of California San Diego, La Jolla, California 92093-0407, United States
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14
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Park CS, Iwabata K, Sridhar U, Tsuei M, Singh K, Kim YK, Thayumanavan S, Abbott NL. A New Strategy for Reporting Specific Protein Binding Events at Aqueous-Liquid Crystal Interfaces in the Presence of Non-Specific Proteins. ACS APPLIED MATERIALS & INTERFACES 2020; 12:7869-7878. [PMID: 31825195 PMCID: PMC7368459 DOI: 10.1021/acsami.9b16867] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2023]
Abstract
Aqueous-liquid crystal (LC) interfaces offer promise as responsive interfaces at which biomolecular recognition events can be amplified into macroscopic signals. However, the design of LC interfaces that distinguish between specific and non-specific protein interactions remains an unresolved challenge. Herein, we report the synthesis of amphiphilic monomers, dimers, and trimers conjugated to sulfonamide ligands via triazole rings, their assembly at aqueous-LC interfaces, and the orientational response of LCs to the interactions of carbonic anhydrase II (CAII) and serum albumin with the oligomer-decorated LC interfaces. Of six oligomers synthesized, only dimers without amide methylation were found to assemble at aqueous interfaces of nematic 4-cyano-4'-pentylbiphenyl (5CB) to induce perpendicular LC orientations. At dimer-decorated LC interfaces, we found that concentrations of CAII less than 4 μM did not measurably perturb the LC but prevented non-specific adsorption and penetration of serum albumin into the dimer-decorated interface that otherwise triggered bright, globular LC optical domains. These experiments and others (including competitive adsorption of CAII, BSA, and lysozyme) support our hypothesis that specific binding of CAII to the dimer prevents LC anchoring transitions triggered by non-specific adsorption of serum albumin. We illustrate the utility of the approach by reporting (i) the relative activity of two small-molecule inhibitors (6-ethoxy-2-benzothiazolesulfonamide and benzenesulfonamide) of CAII to sulfonamide and (ii) proteolytic digestion of a protein (CAII) by thermolysin. Overall, the results in this paper provide new insight into the interactions of proteins at aqueous-LC interfaces and fresh ideas for either blocking non-specific interactions of proteins at surfaces or reporting specific binding events at LC interfaces in the presence of non-specific proteins.
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Affiliation(s)
- Chul Soon Park
- Department of Chemical and Biological Engineering, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Kazuki Iwabata
- Department of Chemical and Biological Engineering, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Uma Sridhar
- Department of Chemistry, University of Massachusetts Amherst, Amherst, MA 01003, USA
| | - Michael Tsuei
- Smith School of Chemical and Biomolecular Engineering, Cornell University, Ithaca, NY 14853, USA
| | - Khushboo Singh
- Department of Chemistry, University of Massachusetts Amherst, Amherst, MA 01003, USA
| | - Young-ki Kim
- Smith School of Chemical and Biomolecular Engineering, Cornell University, Ithaca, NY 14853, USA
- Department of Chemical Engineering, Pohang University of Science and Technology, Pohang, Gyeongbuk 37673, Korea
| | - S. Thayumanavan
- Department of Chemistry, University of Massachusetts Amherst, Amherst, MA 01003, USA
| | - Nicholas L. Abbott
- Smith School of Chemical and Biomolecular Engineering, Cornell University, Ithaca, NY 14853, USA
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15
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Measuring Electric Charge and Molecular Coverage on Electrode Surface from Transient Induced Molecular Electronic Signal (TIMES). Sci Rep 2019; 9:16279. [PMID: 31700032 PMCID: PMC6838146 DOI: 10.1038/s41598-019-52588-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2019] [Accepted: 10/16/2019] [Indexed: 01/05/2023] Open
Abstract
Charge density and molecular coverage on the surface of electrode play major roles in the science and technology of surface chemistry and biochemical sensing. However, there has been no easy and direct method to characterize these quantities. By extending the method of Transient Induced Molecular Electronic Signal (TIMES) which we have used to measure molecular interactions, we are able to quantify the amount of charge in the double layers at the solution/electrode interface for different buffer strengths, buffer types, and pH values. Most uniquely, such capabilities can be applied to study surface coverage of immobilized molecules. As an example, we have measured the surface coverage for thiol-modified single-strand deoxyribonucleic acid (ssDNA) as anchored probe and 6-Mercapto-1-hexanol (MCH) as blocking agent on the platinum surface. Through these experiments, we demonstrate that TIMES offers a simple and accurate method to quantify surface charge and coverage of molecules on a metal surface, as an enabling tool for studies of surface properties and surface functionalization for biochemical sensing and reactions.
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16
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Samieegohar M, Sha F, Clayborne AZ, Wei T. ReaxFF MD Simulations of Peptide-Grafted Gold Nanoparticles. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2019; 35:5029-5036. [PMID: 30869899 DOI: 10.1021/acs.langmuir.8b03951] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Functionalized gold nanoparticles have critical applications in biodetection with surface-enhanced Raman spectrum and drug delivery. In this study, reactive force field molecular dynamics simulations were performed to study gold nanoparticles, which are modified with different short-chain peptides consisting of amino acid residues of cysteine and glycine in different grafting densities in the aqueous environment. Our study showed slight facet-dependent peptide adsorption on a gold nanoparticle with the 3 nm core diameter. Peptide chains prefer to adsorb on the Au(111) facet compared to those on other facets of Au(100) and Au(110). In addition to the stable thiol interaction with gold nanoparticle surfaces, polarizable oxygen and nitrogen atoms show strong interactions with the gold surface and polarize the gold nanoparticle surfaces with an overall positive charge. Charges of gold atoms vary according to their contacts with peptide atoms and lattice positions. However, at the outmost peptide layer, the whole functionalized Au nanoparticles exhibit overall negative electrostatic potential due to the grafted peptides. Moreover, simulations show that thiol groups can be deprotonated and subsequently protons can be transferred to water molecules and carboxyl groups.
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Affiliation(s)
- Mohammadreza Samieegohar
- Chemical Engineering Department , Howard University , 2366 Sixth Street , Washington , District of Columbia 20059 , United States
| | - Feng Sha
- Network Information Center , Xiamen University of Technology , 600 Ligong Road , Jimei District, Xiamen 361024 , Fujian Province, China
| | - Andre Z Clayborne
- Chemistry Department , Howard University , 525 College Street , Washington , District of Columbia 20059 , United States
| | - Tao Wei
- Chemical Engineering Department , Howard University , 2366 Sixth Street , Washington , District of Columbia 20059 , United States
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17
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Nguyen GH, Tran TN, Podgorski MN, Bell SG, Supuran CT, Donald WA. Nanoscale Ion Emitters in Native Mass Spectrometry for Measuring Ligand-Protein Binding Affinities. ACS CENTRAL SCIENCE 2019; 5:308-318. [PMID: 30834319 PMCID: PMC6396573 DOI: 10.1021/acscentsci.8b00787] [Citation(s) in RCA: 72] [Impact Index Per Article: 14.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/29/2018] [Indexed: 05/20/2023]
Abstract
Electrospray ionization (ESI) mass spectrometry (MS) is a crucial method for rapidly determining the interactions between small molecules and proteins with ultrahigh sensitivity. However, nonvolatile molecules and salts that are often necessary to stabilize the native structures of protein-ligand complexes can readily adduct to protein ions, broaden spectral peaks, and lower signal-to-noise ratios in native MS. ESI emitters with narrow tip diameters (∼250 nm) were used to significantly reduce the extent of adduction of salt and nonvolatile molecules to protein complexes to more accurately measure ligand-protein binding constants than by use of conventional larger-bore emitters under these conditions. As a result of decreased salt adduction, peaks corresponding to protein-ligand complexes that differ in relative molecular weight by as low as 0.06% can be readily resolved. For low-molecular-weight anion ligands formed from sodium salts, anion-bound and unbound protein ions that differ in relative mass by 0.2% were completely baseline resolved using nanoscale emitters, which was not possible under these conditions using conventional emitters. Owing to the improved spectral resolution obtained using narrow-bore emitters and an analytically derived equation, K d values were simultaneously obtained for at least six ligands to a single druggable protein target from one spectrum for the first time. This research suggests that ligand-protein binding constants can be directly and accurately measured from solutions with high concentrations of nonvolatile buffers and salts by native MS.
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Affiliation(s)
- Giang
T. H. Nguyen
- School
of Chemistry, University of New South Wales, Dalton Building, Sydney, New South Wales 2052, Australia
| | - Thinh N. Tran
- School
of Electrical Engineering and Telecommunications, University of New South Wales, Sydney, New South Wales 2052, Australia
| | - Matthew N. Podgorski
- Department
of Chemistry, University of Adelaide, Adelaide, South Australia 5005, Australia
| | - Stephen G. Bell
- Department
of Chemistry, University of Adelaide, Adelaide, South Australia 5005, Australia
| | - Claudiu T. Supuran
- Department
of Neuroscience, Psychology, Drug Research and Child’s Health,
Section of Pharmaceutical and Nutraceutical Sciences, University of Florence, Via Ugo Schiff 6, 50019 Sesto Fiorentino, Italy
| | - William A. Donald
- School
of Chemistry, University of New South Wales, Dalton Building, Sydney, New South Wales 2052, Australia
- Phone: +61 (2) 9385 8827. E-mail:
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18
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A dsDNA-lighted fluorophore for monitoring protein-ligand interaction through binding-mediated DNA protection. Sci China Chem 2018. [DOI: 10.1007/s11426-018-9349-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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